Selected Publications (All students and postdocs in Qi lab are underlined)
Anti-CRISPR-Mediated Control of Gene Editing and Synthetic Circuits in Eukaryotic Cells
Nakamura M, Srinivasan P, Chavez M, Carter MA, Dominguez AA, La Russa M, Lau MB, Abbott TR, Xu X, Zhao D, Gao Y, Kipniss NH, Smolke CD, Bondy-Denomy J, Qi LS.
Nat. Commun. 10:194. 2019 Jan 14.
CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming
Liu Y*, Yu C*, Daley TP*, Wang F, Cao WS, Bhate S, Lin X, Still C, Liu H, Zhao D, Wang H, Xie XS, Ding S, Wong WH, Wernig M, Qi LS.
Cell Stem Cell 23(5): 758-771. 2018 Nov 1. (*Equal Contribution)
Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions
Shen JP, Zhao D, Sasik R, Luebeck K, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguez A, Lewis NE, Chang AN, Kreisberg JF, Krogan NJ, Qi LS, Ideker T, Mali P
Nat Methods. 14(6):573-576. 2017 Mar 20.
A Comprehensive, CRISPR-Based Approach to Functional Analysis of Essential Genes in Bacteria
Peters JM, Colavin A, Shi H, Czarny ML, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS*, Huang KC*, Gross CA*.
Cell 165: 1493-1506. 2016 June 2. (*Co-corresponding)
CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs
Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Chan AH, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR.
Cell Stem Cell. 18: 541–543. 2016 Apr 7.
Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise
Sokolik C, Liu Y, Bauer D, McPherson J, Broeker M, Heimberg G, Qi LS, Sivak DA, Thomson M.
Cell Systems. 1(2): 117-129; 2015 August 26.
Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds
Zalatan JG, Lee ME, Gilbert LA, Almeida R, Tsai JC, Whitehead EH, Weissman JS, Dueber JE, Qi LS*, Lim WA*.
Cell 160:339-350; 2015 Jan 15. (*Co-corresponding)
The article is selected as cover art of Cell for that issue. On the cover: CRISPR RNA scaffolds (scRNAs) navigate the genome to direct the CRISPR-Cas complex to specific target genes. Zalatan et al. (pp. 339–350) demonstrate that each scRNA encodes a DNA target and the function to execute at the target, so that sets of scRNAs can be used to generate a synthetic, multigene transcriptional program in which some genes are activated and others are repressed. Artwork by Jennifer Sunami.